TRPV5

transient receptor potential cation channel subfamily V member 5, the group of Transient receptor potential cation channels|Ankyrin repeat domain containing

Basic information

Region (hg38): 7:142908101-142933746

Previous symbols: [ "ECAC1" ]

Links

ENSG00000127412

∙ NCBI:56302 ∙ OMIM:606679 ∙ HGNC:3145 ∙ Uniprot:Q9NQA5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

hypercalciuria, absorptive, 2 (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRPV5 gene.

not_specified (91 variants)
not_provided (9 variants)
TRPV5-related_disorder (2 variants)
Renal_Calcium_Wasting_Hypercalciuria (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRPV5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000019841.7. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar			4
missense	1 clinvar		88 clinvar	8 clinvar	2 clinvar	99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	92	8	2

Highest pathogenic variant AF is 0.000017351751

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRPV5	protein_coding	protein_coding	ENST00000265310	15	25639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.64e-14	0.635	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.193	446	435	1.03	0.0000253	4752
Missense in Polyphen		129	152.05	0.84839		1705
Synonymous	-1.53	194	169	1.15	0.00000935	1494
Loss of Function	1.68	27	38.2	0.707	0.00000217	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000666	0.000663
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000420	0.000416
European (Non-Finnish)	0.000300	0.000299
Middle Eastern	0.000109	0.000109
South Asian	0.000425	0.000425
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Constitutively active calcium selective cation channel thought to be involved in Ca(2+) reabsorption in kidney and intestine (PubMed:11549322, PubMed:18768590). Required for normal Ca(2+) reabsorption in the kidney distal convoluted tubules (By similarity). The channel is activated by low internal calcium level and the current exhibits an inward rectification (PubMed:11549322, PubMed:18768590). A Ca(2+)-dependent feedback regulation includes fast channel inactivation and slow current decay (By similarity). Heteromeric assembly with TRPV6 seems to modify channel properties. TRPV5-TRPV6 heteromultimeric concatemers exhibit voltage-dependent gating (By similarity). {ECO:0000250|UniProtKB:P69744, ECO:0000250|UniProtKB:Q9XSM3, ECO:0000269|PubMed:11549322, ECO:0000269|PubMed:18768590}.;
Pathway: Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Osteoclast Signaling;Vitamin D Receptor Pathway;Stimuli-sensing channels;Ion channel transport;Transport of small molecules;TRP channels (Consensus)

Recessive Scores

pRec: 0.294

Intolerance Scores

loftool: 0.339
rvis_EVS: -0.02
rvis_percentile_EVS: 52.32

Haploinsufficiency Scores

pHI: 0.0742
hipred: N
hipred_score: 0.317
ghis: 0.418

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.773

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Trpv5
Phenotype: digestive/alimentary phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: calcium ion transport;regulation of urine volume;protein tetramerization;protein homotetramerization;calcium ion homeostasis;calcium ion transmembrane transport;calcium ion import across plasma membrane
Cellular component: plasma membrane;integral component of plasma membrane;apical plasma membrane
Molecular function: ion channel activity;calcium channel activity;protein binding;calmodulin binding;metal ion binding